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Chu R, Xu X, Lu Z, Ma Y, Cheng H, Zhu S, Bakker FT, Schranz ME, Wei Z. Plastome-based phylogeny and biogeography of Lactuca L. (Asteraceae) support revised lettuce gene pool categories. FRONTIERS IN PLANT SCIENCE 2022; 13:978417. [PMID: 36311071 PMCID: PMC9597326 DOI: 10.3389/fpls.2022.978417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major Lactuca lineages. The results showed that Lactuca species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce (Lactuca sativa L.) and its gene pool relatives were found to have one unique pseudogene (ψ ndhF), and accD, atpF, cemA, clpP, and rpl22 showed signs of positive selection. Our phylogenomic analysis demonstrated that Lactuca is monophyletic after excluding Lactuca alatipes Collett and Hemsl and AE Lactuca species. AE Lactuca species are morphologically distinct from core Lactuca lineage and need to be excluded from Lactua. The core Lactuca species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of Lactuca, revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.
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Affiliation(s)
- Ran Chu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuemin Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenwei Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yonggui Ma
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Medicinal Animal and Plant Resources of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shixin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Freek T. Bakker
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Roxo G, Moura M, Talhinhas P, Costa JC, Silva L, Vasconcelos R, de Sequeira MM, Romeiras MM. Diversity and Cytogenomic Characterization of Wild Carrots in the Macaronesian Islands. PLANTS 2021; 10:plants10091954. [PMID: 34579486 PMCID: PMC8473144 DOI: 10.3390/plants10091954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/07/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022]
Abstract
The Macaronesian islands constitute an enormous reservoir of genetic variation of wild carrots (subtribe Daucinae; Apiaceae), including 10 endemic species, but an accurate understanding of the diversification processes within these islands is still lacking. We conducted a review of the morphology, ecology, and conservation status of the Daucinae species and, on the basis of a comprehensive dataset, we estimated the genome size variation for 16 taxa (around 320 samples) occurring in different habitats across the Macaronesian islands in comparison to mainland specimens. Results showed that taxa with larger genomes (e.g., Daucus crinitus: 2.544 pg) were generally found in mainland regions, while the insular endemic taxa from Azores and Cabo Verde have smaller genomes. Melanoselinum decipiens and Monizia edulis, both endemic to Madeira Island, showed intermediate values. Positive correlations were found between mean genome size and some morphological traits (e.g., spiny or winged fruits) and also with habit (herbaceous or woody). Despite the great morphological variation found within the Cabo Verde endemic species, the 2C-values obtained were quite homogeneous between these taxa and the subspecies of Daucus carota, supporting the close relationship among these taxa. Overall, this study improved the global knowledge of DNA content for Macaronesian endemics and shed light into the mechanisms underpinning diversity patterns of wild carrots in the western Mediterranean region.
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Affiliation(s)
- Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017 Lisbon, Portugal; (G.R.); (P.T.); (J.C.C.)
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal;
| | - Mónica Moura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO-Azores, Departamento de Biologia, Universidade dos Açores, Rua Mãe de Deus 58, Apartado 1422, 9501-801 Ponta Delgada, Portugal; (M.M.); (L.S.); (M.M.d.S.)
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017 Lisbon, Portugal; (G.R.); (P.T.); (J.C.C.)
| | - José Carlos Costa
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017 Lisbon, Portugal; (G.R.); (P.T.); (J.C.C.)
| | - Luís Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO-Azores, Departamento de Biologia, Universidade dos Açores, Rua Mãe de Deus 58, Apartado 1422, 9501-801 Ponta Delgada, Portugal; (M.M.); (L.S.); (M.M.d.S.)
| | - Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal;
| | - Miguel Menezes de Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO-Azores, Departamento de Biologia, Universidade dos Açores, Rua Mãe de Deus 58, Apartado 1422, 9501-801 Ponta Delgada, Portugal; (M.M.); (L.S.); (M.M.d.S.)
- Madeira Botanical Group, Faculty of Life Sciences, University of Madeira, 9020-105 Funchal, Portugal
| | - Maria Manuel Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017 Lisbon, Portugal; (G.R.); (P.T.); (J.C.C.)
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
- Correspondence:
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Jaén-Molina R, Marrero-Rodríguez Á, Caujapé-Castells J, Ojeda DI. Molecular phylogenetics of Lotus (Leguminosae) with emphasis in the tempo and patterns of colonization in the Macaronesian region. Mol Phylogenet Evol 2020; 154:106970. [PMID: 33031929 DOI: 10.1016/j.ympev.2020.106970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/14/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023]
Abstract
With a wide distribution range including Europe and Asia, Lotus (Leguminosae) represents the largest genus within Loteae. It is particularly diverse in the Mediterreanean region and in the five archipelagos of Macaronesia (Atlantic Ocean). However, little is known about the relationships among the 14 sections currently recognized within Lotus and about the timing and patterns of its colonization in the Macaronesian region. In this investigation, we use four DNA regions (nuclear ribosomal ITS plus three plastid regions) in the most comprehensive sampling of Lotus species to date (some endemic species within the Canary Islands were poorly represented in previous phylogenetic analyses) to infer relationships within this genus and to establish patterns of colonization in Macaronesia. Divergence time estimates and habitat reconstruction analyses indicate that Lotus likely diverged about 7.86 Ma from its sister group, but all colonization events to Macaronesia occurred more recently (ranging from the last 0.23 to 2.70 Ma). The diversification of Lotus in Macaronesia involved between four and six independent colonization events from four sections currently distributed in Africa and Europe. A major aspect shaping the current distribution of taxa involved intra-island colonization of mainly new habitats and inter-island colonization of mostly similar habitats, with Gran Canaria and Tenerife as the major sources of diversification and of further colonization events. Section Pedrosia is the most diverse in terms of colonization events, number of species, and habitat heterogeneity, including a back-colonization event to the continent. Subsections within Pedrosia radiated into diverse habitat types recently (late Pleistocene, ca 0.23-0.29 Ma) and additional molecular markers and sampling would be necessary to understand the most recent dispersal events of this group within the Canary Islands and Cape Verde.
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Affiliation(s)
- Ruth Jaén-Molina
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain.
| | - Águedo Marrero-Rodríguez
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain
| | - Dario I Ojeda
- Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway
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Romeiras MM, Pena AR, Menezes T, Vasconcelos R, Monteiro F, Paulo OS, Moura M. Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity. Int J Mol Sci 2019; 20:E2782. [PMID: 31174340 PMCID: PMC6600550 DOI: 10.3390/ijms20112782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/16/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022] Open
Abstract
Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.
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Affiliation(s)
- Maria M Romeiras
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Ana Rita Pena
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Tiago Menezes
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
| | - Raquel Vasconcelos
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Filipa Monteiro
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Mónica Moura
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
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